Journal Article

Searching protein structure databases with DaliLite v.3

L. Holm, S. Kääriäinen, P. Rosenström and A. Schenkel

in Bioinformatics

Volume 24, issue 23, pages 2780-2781
Published in print December 2008 | ISSN: 1367-4803
Published online September 2008 | e-ISSN: 1460-2059 | DOI:

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The Red Queen said, ‘It takes all the running you can do, to keep in the same place.’ Lewis Carrol

Motivation: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive—thorough but slow—search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC.

Availability: The Dali server for protein structure database searching at is running DaliLite v.3. The software can be downloaded for academic use from


Journal Article.  1576 words. 

Subjects: Bioinformatics and Computational Biology

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